Few microsporidia have been reported from whitefish species (subfamily Coregoninae). For the most part, these microsporidia have been incompletely described. In a survey of parasites of mountain whitefish Prosopium williamsoni collected from Kootenay Lake, British Columbia, we encountered an unusual microsporidium infecting the endomysium of the skeletal musculature. Spores were uninucleate, ovoid to pyriform, and were 5.6 (5-7) microm x 3.2 (3-4) microm with 13-16 coils in the polar filament. We describe here this organism as a new species based on its site of development and its relationship among fish microsporidia based on small subunit ribosomal DNA sequence data, i.e., our analysis showed that it is not closely related to other microsporidia for which ribosomal DNA sequence is available thus far.